Apollo Genome Annotation Curation Tool

Description

View and analyze genome annotation. Apollo is a genome annotation viewer and editor. It was developed as a collaboration between the Berkeley Drosophila Genome Project (part of the FlyBase consortium) and The Sanger Institute in Cambridge, UK. Apollo allows researchers to explore genomic annotations at many levels of detail, and to perform expert annotation curation, all in a graphical environment. It was used by the FlyBase biologists to construct the Release 3 annotations on the finished Drosophila melanogaster genome, and is also a primary vehicle for sharing these annotations with the community. The Generic Model Organism Database (GMOD) project, which aims to provide a complete ready-to-use toolkit for analyzing whole genomes, has adopted Apollo as its annotation workbench. Apollo is a Java software that can be downloaded and run on Windows, Mac OS X, or any Unix-type system (including Linux).Apollo is a Java software that you can download and run on your computer (Windows, Linux, or Mac OS X--earlier Mac versions are not supported). You can get Apollo here. When you install Apollo, a JVM is bundled with it, unless you are on Mac OS X.Apollo uses a lot of memory, largely due to the sheer size of the annotation data. In order to use Apollo, your computer will need to have at least 256Mb of RAM. Moreover, even if you have that much memory, you will probably find that if you try to run more than one instance of Apollo at the same time, performance will suffer. Also note that if you load a very large region, Apollo will use up more memory.
Keep in mind that other applications running on your computer also use memory, so you will get better performance if you shut down other applications (Photoshop, Word, etc.) before you launch Apollo.Apollo checks twice a minute to make sure you still have enough free memory. If the free memory is getting very low (less than 5% of the the value defined as "Memory" in apollo.cfg), you will get a warning. If you have done or are planning to do any editing, you should save your work and then quit and restart Apollo.If you load many large regions into Apollo (such as cytological bands), it is possible that it will run out of memory despite the memory checks. Usually the behavior you'll see if this happens is that it will freeze up during loading, but sometimes other things will start to go wrong. If you then look at the Java console, you may see "java.lang.OutOfMemoryError". If this happens, you should exit Apollo and restart.Requirements:
* Java

Published By:apollo.berkeleybop.org

License Type:Freeware

Date Added:10 October, 2012

Version:1.11.6

Price:Free

Downloads:2

Size:17.2 MB

Platform: Macintosh

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